From 4d50c5af34bbc5a33e3ed7ba39755e9e8ed07895 Mon Sep 17 00:00:00 2001
From: William Patton <wllmpttn24@gmail.com>
Date: Mon, 19 Aug 2024 07:35:01 -0700
Subject: [PATCH] always use cyto masks and plot membrane channel

---
 solution.py | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/solution.py b/solution.py
index 61f8855..a4e305f 100644
--- a/solution.py
+++ b/solution.py
@@ -171,10 +171,10 @@ def compute_sdt(labels: np.ndarray, scale: int = 5):
 idx = np.random.randint(len(samples) // 3)  # take a random sample.
 img = tifffile.imread(os.path.join(root_dir, f"img_{idx}.tif"))  # get the image
 label = tifffile.imread(
-    os.path.join(root_dir, f"img_{idx}_nuclei_masks.tif")
+    os.path.join(root_dir, f"img_{idx}_cyto_masks.tif")
 )  # get the image
 sdt = compute_sdt(label)
-plot_two(img[0], sdt, label="SDT")
+plot_two(img[1], sdt, label="SDT")
 
 # %% [markdown]
 # <div class="alert alert-block alert-info">
@@ -232,9 +232,7 @@ def __init__(self, root_dir, transform=None, img_transform=None, return_mask=Fal
             img_path = os.path.join(self.root_dir, f"img_{sample_ind}.tif")
             image = self.to_img(tifffile.imread(img_path))
             self.loaded_imgs[sample_ind] = inp_transforms(image)
-            mask_path = os.path.join(
-                self.root_dir, f"img_{sample_ind}_nuclei_masks.tif"
-            )
+            mask_path = os.path.join(self.root_dir, f"img_{sample_ind}_cyto_masks.tif")
             mask = self.to_img(tifffile.imread(mask_path))
             self.loaded_masks[sample_ind] = mask
 
@@ -293,9 +291,7 @@ def __init__(self, root_dir, transform=None, img_transform=None, return_mask=Fal
             img_path = os.path.join(self.root_dir, f"img_{sample_ind}.tif")
             image = self.to_img(tifffile.imread(img_path))
             self.loaded_imgs[sample_ind] = inp_transforms(image)
-            mask_path = os.path.join(
-                self.root_dir, f"img_{sample_ind}_nuclei_masks.tif"
-            )
+            mask_path = os.path.join(self.root_dir, f"img_{sample_ind}_cyto_masks.tif")
             mask = self.to_img(tifffile.imread(mask_path))
             self.loaded_masks[sample_ind] = mask
 
@@ -422,7 +418,7 @@ def create_sdt_target(self, mask):
 image = np.squeeze(image.cpu())
 sdt = np.squeeze(sdt.cpu().numpy())
 pred = np.squeeze(pred.cpu().detach().numpy())
-plot_three(image[0], sdt, pred)
+plot_three(image[1], sdt, pred)
 
 
 # %% [markdown]
@@ -577,7 +573,7 @@ def get_inner_mask(pred, threshold):
 # %%
 # Visualize the results
 
-plot_four(image[0], mask, pred, seg, label="Target", cmap=label_cmap)
+plot_four(image[1], mask, pred, seg, label="Target", cmap=label_cmap)
 
 # %% [markdown]
 # <div class="alert alert-block alert-info">
@@ -770,7 +766,7 @@ def create_aff_target(self, mask):
 )
 idx = np.random.randint(len(train_data))  # take a random sample
 img, affinity = train_data[idx]  # get the image and the nuclei masks
-plot_two(img[0], affinity[0] + affinity[1], label="AFFINITY")
+plot_two(img[1], affinity[0+2] + affinity[1+2], label="AFFINITY")
 
 # %% [markdown]
 # <div class="alert alert-block alert-info">
@@ -809,6 +805,7 @@ def create_aff_target(self, mask):
 loss = torch.nn.MSELoss()
 
 optimizer = torch.optim.Adam(unet.parameters(), lr=learning_rate)
+plot_three(image[1], mask[0] + mask[1], pred[0 + 2] + pred[1 + 2], label="Affinity")
 
 for epoch in range(NUM_EPOCHS):
     train(
@@ -838,7 +835,7 @@ def create_aff_target(self, mask):
 mask = mask.cpu().numpy()
 pred = pred.cpu().detach().numpy()
 
-plot_three(image[0], mask[0] + mask[1], pred[0] + pred[1], label="Affinity")
+plot_three(image[1], mask[0] + mask[1], pred[0] + pred[1], label="Affinity")
 
 # %% [markdown]
 # Let's also evaluate the model performance.